The storm in the Kerch Strait killed at least six sailors, sank four ships and split an oil tanker.
"The environmental damage caused by ships sinking in the Kerch Strait is estimated by Rosprirodnadzor at about 6.5 billion rubles," Yury Trutnev said in a statement released by the ministry's press service.
A member of the WWF volunteer group said the number of birds killed by the oil spill in the Kerch Strait will keep growing.
At least 2,000 metric tons of fuel spilled into the Kerch Strait killing several thousand birds, including many endangered species. Sulfur is currently reported to be leaking from one of the sunken ships.
"Birds stained with fuel oil have virtually no chance of survival if no one helps them," Valentin Kozlitin, the chief veterinary doctor at the Moscow zoo, told RIA Novosti following his return from the disaster area.
Earlier reports said some 30,000 birds had died as a result of the oil slick but Kozlitin warned the number of dying birds will increase as their migration routes cross the disaster area.
He said there is still a chance to help the birds arriving at the oil slick site. "The authorities are taking no steps to rescue the birds and, on the contrary, are restricting and hampering the work of a few volunteers," Kozlitin added.
He said birds are dying of dehydration, hypothermia and starvation. The Russian Bird Protection Union said earlier birds stained with fuel oil should be washed with cleaning agents and kept warm.
Ukrainian Prime Minister Viktor Yanukovych urged on Wednesday an independent probe into the Black Sea ecological disaster.
The prime minister also said that a group of 20 Russian and Ukrainian environmental experts was working alongside a European Union mission in the Strait.
He also said the group had requested help from Norway, which reportedly has a ship capable of lifting oil from the seabed.
The Russian emergencies service regional press center said that about 2,000 tons of oil product waste had been removed from the coastline in the past 24 hours, bringing the total amount to approximately 17,500 tons. The clean up operation of the coastline is continuing, although ongoing storms have caused some recontamination.
According to the ministry, one kg of fuel oil turns into 200 kg of oil product waste after mixing with sand, algae and litter.